Life in a Bottle
by ancientlybroken
Summary: AU Sheppard gets pulled in an alternate reality. Enemies are friends and friends are enemies. Can he get home? Will he even want to? Rated T to be safe and for future violence and language.
1. Chapter 1

First Fic. yahoo!!

This will be a Sheppard centric story, multi chapter so give it a chance.

I odn't own any of the characters, don't resort to legal measures as it would yeild little fruit.

* * *

This was the story of how he died.

It was a day for cliché's. The sky was overcast and the waves were choppy. It could even be called a dark and stormy night, except that it was midday. The air was alive with the smell of ozone, lightning could be seen far away, jagged fissures in the slate colored sky. It had not started to rain over the city, but it would. It was going to rain cats and dogs. Weathermen would still have gotten that wrong, of that he was certain.

Col. John Sheppard stepped back from the edge of his balcony. It was his because he was one of the few who ever went there. It was the place he had first seen the city from, all those years ago when the city was still under water. By unspoken law it had become his. It was his own sanctuary, a place to be alone with his thoughts. More often than not his thoughts were dark. Today they were morose.

It was fitting for such a dark day.

He remembered the dead. There were so many. His hazel eyes stared down into the inky darkness of the turbulent water, trying to remember the first. The first casualty in a long line of casualties, in a never ending line of dead.

Who had it been? A woman. Yeah, a woman, in the military, if his memory was accurate, definitely military. Maybe he should have been glad it hadn't been one of the civilians. Somehow he couldn't muster the sarcasm that usually kept the horror at bay today. He could see her face, but the name escaped him. It had been 4 years ago. It was a long time to remember someone. An eternity in this place. He used tricks he had learned as a child. Focus on one or two details and let the rest flow.

She had had blonde hair. Pretty smile. Yeah her smile was nice, great teeth. He waited, not forcing it, knowing his memory would come to him at some point.

Lightning flashed and the thunder rode quickly in its wake. The storm was almost there. Weir hadn't raised the shield, and he knew she wouldn't. A bit of water they could handle, some rough seas were a bit inconvenient, but not life threatening. Running out of power, a constant fear with already taxed ZPM's, well that was something no one wanted to think about.

The lightening lit up the sky once again, blinding him for a moment. It was then he remembered.

Cadman. Laura Cadman.

Yeah that was her name. He couldn't remember how she had died exactly. Perhaps that was a small mercy, one for which he was grateful. Laura Cadman, a lieutenant, competent. The first to fall in this brutal war. Young, they were always too young, even when they were old. No one deserved to die like this, here, so far from home.

Was it even a war anymore?

He closed his eyes and tilted his head back, catching the first fat raindrops as they lost their battle with gravity and fell from the clouds. The deck shook with the force of thunder and the heavens opened, spilling rain in a drenching deluge. In seconds he was soaked, barely above freezing rain water running across his face. Oddly he didn't mind, it was refreshing, even if it was a bit painful, and he stood a moment in the cleansing rain. If only all of their problems could be as easily washed away.

His comm. Unit chirped in his ear and he sighed, the weight of the world reasserting itself in one single soft sound. Even the great storm couldn't drown out the call of his responsibilities, and they were many.

"Hell, been away long enough as it is." He said to the storm and turned and went inside, the door opening for him at his approach.

"Sheppard here."

"Come to the Gate room Col, we have a situation." Dr. Weir, head of what was left of the Atlantis expedition, ordered.

He sighed again, weary. "On my way."

There was _always_ a situation. They were running out of power, food, clean water, medicine, just to name a few. They had been found. Again. His insides turned to ice.

_Gods above and below, hell anyone who'll listen, not that, not so soon._

It was a silent prayer and one he did not expect answered. One thing had been made abundantly clear to him. Those with the power to did NOT intervene. However much they had been revered, the ancients were not gods, and if they were it was a cruel cosmic joke. If there were gods, real ones like they wrote about in Greek Mythology or used to worship in beautiful cathedrals on Earth, they were so far away they couldn't hear him. That was the cold hard truth.

But it didn't stop him from praying.

Or believing in miracles. He had seen a miracle. Just one. It hadn't been a cunning bit of technology or that last minute save that kept them alive for one more day. Those were plain dumb luck. His miracle was something more, and very simple. He hoped to see another in 8 months or so.

His thoughts did not linger there for long, the darkness clinging to the walls of the corridors seemed to seep into his head and prevent him from rising above the gloom. His thoughts remained dark.

His thoughts stayed with the dead, the old and the new. It still hurt. He took their deaths personally, a testament of his failure. His thoughts turned to his most recent failure. Major Evan Lorne, his second in command, a trusted friend.

He brushed the comm. in his hear. "Dr. Beckett."

"Aye, Col Sheppard." The Scotsman's brogue came through.

"How's Lorne doing?"

There was a loud sigh. "We're just getting ready to go into surgery. We'll know soon."

Sheppard tried to keep his voice even. "Keep me posted."

"Will do son, Carson out."

Lorne had been on a simple recon mission. They had received reliable, what they had believed to be reliable, Intel on a ZPM, and it was too good to pass up. They currently had 3, but 3 was the bare minimum they needed. Power was something they always required more of.

It had been his call. He had sent Lorne, the man was capable and could handle anything that came his way. It had been a set up. In hindsight he wished he had gone himself, not that things would have ended differently, but it was better him than anyone else. Their allies had sold them out. It had happened before. Honor was honor and it was in short supply these days.

It had been particularly bad this time. They had been ambushed and had to retreat through a mine field back to the gate. It had become one of the enemy's trademarks. Go through a gate and meet no resistance and everything looked just hunky dory. Then, while the teams were off exploring, negotiating, looking for whatever the reason for the mission dictated, they would set up these mobile mine fields. When they tried to go back the way they came, well there was a nice surprise waiting.

The entire team had been wounded, but Lorne had taken the worst. Lorne guarded their flank and had triggered the mine field as his team went threw the gate. The resulting concussive blast had discouraged pursuit, but had also thrown Lorne threw the gate at a tremendous velocity, not to mention the fire ball that travelled with him.

Long ago the Atlantis team had set up several beta sites, neutral unpopulated planets that were staging grounds. All outgoing teams went to Beta sites and then on to alternate destinations and same in reverse order. It kept the location of Atlantis itself safe.

Lorne had had to wait for the energy of the blast he caused to quit feeding the gate so it could close before his team could dial home. It had taken more than 20 minutes and that 20 minutes nearly cost the Major his life. He sustained severe burns to his hands and left arm, a major head injury and several broken bones, a punctured lung and he was bleeding internally. Sheppard was no doctor, but even he knew this was going to be close.

Lorne was a hero. He saved the lives of his team. Unfortunately, Lorne was one of a select few who they just simply could not afford to lose.

_Lorne, of all the damned luck._ Sheppard thought. There were only 4 left, only 4 who had the ancient gene, and the people within the city relied on these 4 for their lives. Without them, they were defenseless. And 2 of them weren't even military. Carson Beckett and his sister Ava. Both doctors, both working themselves into the ground. Both never complaining, just making due with limited medical supplies and limited staff and a never ending stream of injured making their way through their infirmary.

4 small lives away from being parked in this massive city, unable to move, unable to fight, the proverbial sitting duck.

His feet took him automatically to his destination, a path so familiar he didn't need to think about it anymore and his mind was free to wander and remember, remaining as dark as the sky outside.

Lists of the dead. There were so many. Faceless soldiers and scientist who had not expected the desperate fight for survival, and been crushed under the juggernaut of war. Teylas' s people had been hunted to near extinction. He remembered Halling. He remembered finding his broken body amongst the ruins of a tiny settlement.

So many others, just gone. Ford, lost early on. The pain was still fresh. Then there was Col Caldwell, bought his ship, Deadalus, time to get away with a suicide mission, ramming a nuclear bomb down their throat, and hoping they choked on it. Sheppard would never admit it, but he missed the older man. His experience would have been invaluable.

He should have felt anger at all the waste, but anger had died a long time ago. All that was left in its wake was defeat. There weren't enough of them left to mount that one final heroic battle. There was no going out in a blaze of glory for them. Theirs would be a slow agonizing death as supplies ran low and trust ran thin. Trade would stop, supplies would be scarce and then on one fateful day there would just not be enough, and it would end. That was how he saw it ending.

But not today.

And not tomorrow.

It was a date in the future, months maybe even years down the road. He momentarily wondered if he could start a pool, betting on the exact date of their demise. _Nah, Elizabeth would probably shoot me herself for that one._ He chuckled. She wouldn't be the only one. He could think of a few people who would join that firing squad.

He rounded the last corner and took the stairs two at a time. He stowed the darkness for later. Now he had to be what everyone needed him to be, the hope filled military commander of Atlantis. He found that persona and slapped it on, sure and confident.

"So what's the problem this time?" He said easily, hands hanging casually at his sides.

There was silence as Zalenka looked to Sheppard and Weir and she nodded. "An unknown signature has appeared at the far edge of the solar system."

"What do you mean unknown?" Sheppard's eyes narrowing.

"Meaning we have no idea what or who it is. We've never seen a hyper drive signature like it before."

Sheppard turned looking around the circle of the leaders of this "expedition". Weir looked worried, and haggard. Zalenka had bits of hair standing up in strange places and his glasses were a bit lopsided. He wondered when the last time the Czech scientist had slept.

Michael spoke up, his odd musical multi-toned voice cutting through the tense silence. "It is unfamiliar to us as well."

That did not bode well. There was silence for a moment as everyone looked at the small red dot at the edge of the solar system, willing it with their eyes alone to just keep on sailing right on by. Finally he broke the tense silence.

"Well, 2 possibilities. One: someone new and powerful, may be on our side." It was a possibility but the look that passed from Zalenka and Michael said it all. If it was an ally where the hell had they been all this time. "Or, two,_ they've_ come up with something knew." Everyone knew who _they_ were.

"So either we sit here, wait and hope, or we pull up anchor and find somewhere else." Weir stated.

They had been down this road before. Too many times they had waited too long, hoping they wouldn't be seen, that the cloak would be enough. It had cost them in the past.

An annoying beeping started, coming from the computer monitor. Beeping in general was bad. It was like a bad episode of Star trek. Things only beeped when the ship was about to blown up, or the previously sexy peaceful aliens were insulted by some tradition no one knew about that had been disrespected, blah blah blah, ending in total destruction in 10 seconds.

. "No. no. no no no no." Zalenka said, Sheppard nearly smiled. Zalenka slipping into one of his McKayisms.

"What?" Weir asked, her shoulders tense and her face pale.

"They've picked up speed, and are heading straight for us."

_Great._ "Well that settles it. I'll head to the chair and get things going, time to leave." He had taken 5 steps towards the stairs when Zalenka spoke again.

"You don't understand."

"Zalenka!" he barked, he'd apologize later.

"Based on their current speed and the acceleration, and they are still accelerating"

"RADEK!"

"They will be here in less than 30 minutes."

_Oh God. _It took at least 30 minutes to ready the star drive for use. It had started taking longer as they had used it so often and, well 10 000 year old systems didn't last forever. The silence was absolute as everyone digested that information. They all knew how long it actually took to get airborne. They knew how long they really could last against them when it turned into a fire fight, once they were within weapons range.

"right". Sheppard said, digesting the new information and moving on. He brushed his ear piece. "Ava." He said.

"Go ahead." Her bright voice responded immediately.

"We have a situation, get to the chair and ready the star drive."

There was a pause, and finally an exhausted sigh. "On it."

"Ava."

"Yes."

"It needs to be done in record time."

There was another pause, he could imagine the look on her face, green eyes growing wide and a grim determination setting her mouth into a frown. He heard the baby coo in the background.

"Better get to it then." Was the reply and she was gone.

"I assume you have a plan." Weir said folding her arms and trying her best to look annoyed.

"I always have a plan." And he flashed his best cocky grin, selling it for all he was worth.

* * *

Sheppard was in the jumper bay. By his count he had 20 minutes until the unidentified vessel arrived.

"You don't have a plan." A musical voice intoned behind him.

"Of course I have a plan." He said not turning around and looking at the other occupant of the craft.

"In all of the years I have known you, John Sheppard, you have never had a plan."

Now he did turn and look, fixing Todd with his best bland _I have no idea what you mean_ look. Todd just looked back, pale features gleaming in the half light waiting. The damn wraith had more patience than… Job.

"All right, I don't have a plan, but I will have one before that ship gets here." Todd, just grinned, a truly ferocious expression on a Wraith, and laughed his odd musical laugh. He moved forward and took the seat next to Sheppard.

"What the hell do you think you are doing?"

Golden eyes sparkled. "I am coming with you."

"No."

"Whatever last minute plan you concoct will be easier to accomplish with an extra set of hands." Todd stated.

There was a pause, a silence that was heavy with intention and words that would never be spoken.

"I'm most likely not coming back." Sheppard said simply. Todd smiled again, more a baring of teeth, than a real smile, but a smile none the less.

"Ah, so you do have a plan then. Excellent. This should be most entertaining." Todd still made no move to leave. Sheppard never would have admitted it, but he was suddenly very grateful to the man at his side. An unlikely ally, an unlikely friend.

"Well when you put it that way…" Sheppard responded with a wry grin.

* * *

The alien ship continued to accelerate. It was an insane speed for sub light engines. Zalenka shaved additional time off his original estimate of 30 minutes. If they were lucky, and they seldom were, the alien vessel would be within weapons range in 22 minutes, give or take a minute or two.

Weir stood on the balcony, overlooking the gate, arms crossed across her breast, an uneasy expression fixed to her face. Her eyes weren't focused on the organized chaos below her. The city was being evacuated to a Beta site, all nonessential personnel. The Deadalus and the Phoenix had already been sent ahead to the Beta site and they would guard the refuges until the all clear was given and Atlantis was safe in its new home.

The Persephone would remain with Atlantis, secure their escape. It was the ship they could afford to lose of the 3. Persephone had seen more than her fair share of battle and over the last year they had reduced her to more of a transport/ storage ship and were slowly cannibalizing the ship for spare parts to repair the other two.

"You are worried."

She inhaled sharply, "Michael, you startled me." She said. She couldn't' bring herself to smile. The years of running and hiding, the years of such terrible loss were taking their toll. "Just lost in my thoughts I guess. I'll feel better once we are in the air and far away from here."

He placed a hand on her shoulder, a hand that used to be a feeding hand, and now was just a hand like hers. He said no words just a reassuring pressure.

"Has Dr. Beckett been evacuated."

She frowned, "No, Major Lorne had just gone into surgery and there is no way to safely move him."

At that exact second the skeleton crew of the Persephone materialized on the gate platform.

"Major Harris, what are you doing here?" She asked from her bird's eye view of the room.

"Reporting as ordered ma'am."

She looked puzzled. " I didn't give that order Major."

Harris looked back at her. "But the Col." He started to say.

She held up a hand silencing him with a gesture. "Chuck get me on comm. with Persephone, now."

* * *

Sheppard looked at the device and then looked at Todd.

"Why couldn't he have just had a big red button that said 'push me'."

Todd shrugged and continued looking threw pages of code.

Only minutes left.

"Col Sheppard respond."

He wasn't surprised.

"Dr. Weir."

"What are you doing?"

"Well, Todd and I just felt like taking a pleasure cruise, see the sights." A proximity alarm sounded.

"What is that?" Weir shouted to be heard above the din.

"Alien ship closing fast, Sheppard. They have launched some kind of missile." Todd said ignoring Weir for now.

"Target?" Sheppard demanded and seized the controls of the ship.

Todd was silent for a moment. "Atlantis."

"Elizabeth…"

"Yes we copy."

"How long till the star drive is online?"

There was silence and then. "5 more minutes." He thought it might be Chuck.

He looked at Todd, who simply nodded.

"Right, my plan. We have the McKay."

"What, are you insane. No one knows if that thing will even work." Zalenka this time.

"It'll work." Sheppard said with confidence. The McKay was the last great invention of one Dr. Rodney McKay, self proclaimed smartest person to ever live. The device was essentially a bomb, but the rough gist of it was that it created an artificial black hole. If it was detonated near an enemy ship it would destroy the ship. The only side effect was that it would probably destroy the planet as well, and all too likely the solar system too. A singularity was a powerful thing, and there was no way to predict how big it would be.

"Yes but even if it works." Zalenka continued in panicked tones.

"I know. Look we are out of time."

There was a loud explosion and muffled shouting on the other end.

"What was that?" Sheppard demanded.

"Status!" Weir shouted.

"The gate is offline and that blast reduced the shields to" there was a pregnant pause. "… 45%" Zalenka answered quickly.

"45%?!" shock coloring weir's voice. The shields wouldn't survive another hit. If the shields went down, engaging the star drive would be pointless, the vacuum of space would kill everyone anyway.

"Elizabeth, you guys need to get out of there."

"I know!!! We need more time!"

Todd brought up the viewing screen. A blue and green orb materialized before them and it was such a beautiful scene, the clouds isolated to one part of the planet, the rest was under clear skies. The planet turned slowly, at peace, unaware of the fight for life taking place just outside of its atmosphere.

"Does this bucket of bolts still have functioning weapons?"

Todd quickly moved to another consol.

"According to this it does, but limited. Asgaurd weapons are only at 15% and there are 12 torpedoes and the rail guns, half are functioning." Sheppard thought for a moment.

"Shields?"

"No."

"Of course, that would make this easy." Todd laughed darkly. "Elizabeth how long do you need?"

There was muffled shouting and words exchanged, then "6 minutes." That was a long time.

"We're going to buy you some time." This was along the lines of the overall plan. Using the McKay was almost certain death anyway, what was a few extra minutes of fire fight.

"You don't have to do this, we'll find another way." She pled.

"Elizabeth, just be ready. We're setting the timer on the McKay for… 7 minutes. That should be enough time for you to get away."

"Col, you don't have to do this." Elizabeth begged. He didn't respond to that.

"Comm. is going dark, good Luck Atlantis."

"John!"

"Sheppard out." And he turned off communication with the city, went back to looking at the impressive vista of the planet.

There was a moment of silence. Digesting that this was indeed "it".

"Better set that timer, you know how to do that right?" Todd grunted and complied.

"7 minutes and counting."

"How long until we are in weapons range of the other vessel?"

Todd glanced at the consol. "1 minute and 12 seconds."

* * *

6 minutes flew by in the blink of an eye. The Persephone held up under the onslaught of the alien vessel. Predictably the Asgaurd weapons had no affect and they had tried to siphon the power there to the shields with limited success.

Sheppard flew and Todd controlled weapons, releasing everything they had to give Atlantis that few more minutes.

The ship shook with the force of another direct hit and sparks shot out of the ceiling, a fire spreading nearby. They were too busy to deal with the fire. Weapons were offline.

"Sheppard we are venting atmosphere."

"Can you seal off the area."

"Controls are not responding."

"How much longer?" He didn't really care if it was until the McKay blew or they lost all breathable air.

"1 minute for the McKay."

"Right." He angled the ship and plotted an intercept course. "can we see the city on that?" Todd said nothing, but brought up a static filled image of Atlantis, glowing with the orange light of the shield. He could almost feel it humming with power as the star drive came online.

"30 seconds."

There was a bright light and suddenly the city shuddered and began to rise. "Come on Ava fly that thing, move!" He yelled at the screen.

"15 seconds."

Sheppard had time for last thoughts.

Atlantis was now down to 3. Only 3 stood between life and death and he was sorry he left them shorthanded.

He wished he had had a chance to say goodbye.

The last thing he saw before the end was Atlantis in all her glory reaching for the stars, her golden spires gleaming in the light of the alien sun. She was beautiful.

At the exact instant Atlantis cleared the atmosphere and entered hyperspace, the proximity alarms sounded. The alien vessel was large in the screen.

"Well, I guess this is It buddy." Sheppard said.

"It has been an honor John Sheppard."

"Yeah."

There was only light. Endless light.

The McKay exploded in a brilliant flash of fire and splintering of metal. As the singularity grew, the explosion collapsed in on itself, dragging everything in with it, Persephone, the alien ship, and eventually the planet itself. Thousands of years in the future the sun would begin to fail and particles of hydrogen and helium would begin their long fall into the gapping maw of the vortex. For now it had accomplished its goal. The alien ship did not peruse, Atlantis had escaped.

The cost was terribly high.

John Sheppard, Colonel in the United States Air Force died, on Sept 23, at 13:15 hours, as Earth reckoned time. He was 41 years old. He didn't die alone and his death was heroic. He was survived by his wife, Ava Sheppard and their son, Ronon Rodney Sheppard aged 2 months.

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There it is first Chapter, will get the next one up ASAP. review let me know what ya think.


	2. Chapter 2

Thanks to those of you who reviews, made me happy and gets me to update faster.

I don't own Stargate wish I did.

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"Run damn it." Sheppard yelled, stopping to provide cover fire for a second before sprinting off again into the woods.

"This can't be good for my heart!" McKay yelled back.

"And dying is?" Ronon shouted from up ahead.

"Well when you put it that way." And McKay stoically trotted after the big warrior.

The mission had gone to hell in a heartbeat. The people had seemed friendly enough, though Teyla had never heard of them. Urosian's. They were a simple people, in a mostly agrarian society. They were deeply religious, and refused to discuss their beliefs with outsiders. Fair enough, no preaching of the good word seemed almost too good to be true to Sheppard, and McKay was downright ecstatic. Everyone knew what McKay thought about "spiritual" matters. Hocus pocus and pipe dreams; opiate of the masses.

Sheppard had always thought that was harsh, but wasn't sure which side of the debate he really fell on so he held his peace. Not easy to do with McKay around.

Oddly enough this current situation had nothing to do with Rodney and his mouth. It was Teyla. The woman was so diplomatic that she usually was able to talk them out of these situations, not get them into one. Teyla had been simply wandering round the market, looking at the town's homemade crafts when she happened to bump into one of their holy men. He immediately accused her of deliberately trying to stir impurity in him. She of course denied it and tried to apologize. It didn't matter. The preist demanded compensation for his loss of holiness. How you calsute the value of holiness was beyond Sheppard, but he had learned logn ago to just roll with it. The high Pirest determined that Tyela was impure and there was a need for a cleansing ceremony, to purge Teyla of her sinfulness and the town of her taint.

They assured sheppard that the cleansing was harmless.

The cleansing ceremony seemed innocent enough. A little bit of holy water and the High Priest chanting words that sounded strangely familiar. The language was deep and guttural punctuated by hissing. Teyla had dutifully knelt before the priest head down in contrition, her constant semi annoyed glances toward the rest of the team her only indication that this really made her uncomfortable. The Priest passed his hands over Teyla's head and then held his palms to the sky, presumably asking their gods for forgiveness of this woman's sins or something along those lines. Then he lifted his hands to the crowd, palms out, revealing some kind of device strapped to his hand. It slipped over the fingers like a glove and there was a button in the center of his hand, a soft inert blue color. The Priest bowed his head and brought his hands together, pushing on the blue device in the process.

Perhaps the situation could have been salvaged, no harm done after all. Teyla was fine; the High priest looked positively radiant at the completion of his duties and was in the middle of helping Teyla to her feet when Rodney's shrill voice broke through the soft murmuring of the crowd.

"HOLY SHIT IT'S A WRAITH TRACKING DEVICE!"

Predictably it went downhill from there.

The simpletons had been better armed than Sheppard had believed possible. Wraith stunners and a variety of projectile weapons, not to mention some kind of blow dart that caused numbness and eventual paralysis. They only knew that because Teyla had been hit almost instantly and gone down like a tree within seconds. Ronon had her slung over his shoulder like a sack of potatoes as he set a quick pace back to the gate. They ran, ears straining to catch that first whine of a dart's engines.

Sheppard ducked as a stunner blast flew into the tree where his head had been a second earlier. "McKay, where's the gate!"

"Almost there," he panted, " 500 m, that way, "McKay pointed straight ahead and to the left a bit, " and then down a ridge to the gate plain."

There was no need for more words. Ronon took point, Teyla still unconscious and Rodney made a great attempt at looking brave, but his eyes were just too wide.

The 500m through the trees passed in silence and was quick. The ridge was another story.

"How do we get down that?" McKay shouted hysterical. Sheppard wondered the same thing looking a stepp descent. Ronon gave it a look that said, _you won't stop me damn mountain _and began to half slide and half walk down, one arm out for balance and a vice like grip on his friend.

McKay just kept staring, squeaks that probably were words coming out if his mouth ever so often. Sheppard grabbed his tack vest and shouted "MOVE!!" and they began their own descent together. The ridge/ hill was mostly a wind weathered outcropping of shale and dirt, a few trees clinging desperately to whatever they could amongst the rubble. Sheppard kept a hand on McKay just to keep him on his feet and continued moving forward.

It happened really fast. McKay went down, his ankle rolling on something hidden under the shale. Sheppard, hand still on the scientist, went down with him. They rolled and bounced down the remaining 100 feet, getting real personal with bits of shale, rock, gravel, and fragile saplings. Together they even managed to trigger a small rock slide and wound up half buried in the rocks.

Ronon could only watch and continue to pick his way down the hill to his friends.

"Sheppard, McKay, you alright!?" He shouted as he got closer.

"We're alive if that's what you mean?" Sheppard yelled back.

"Speak for yourself." McKay moaned. They both pulled themselves out of the rocks and surveyed the damage. McKay had a good cut along his hairline, painting his face a grisly red, but everything else seemed to function, until he tried to put weight on the ankle that caused this all to begin with. "I think I sprained my ankle." Sheppard had fared better, just a bunch of scraps and what he knew would be deep tissue bruises tomorrow, but for now adrenaline would be enough to keep him on his feet.

They could hear the townspeople coming. The remaining distance to the gate was on a flat exposed piece of ground, 50 m to the DHD, and then to the gate to home, and safety. Teyla moaned, but made no other signs of coming out of it.

"If we wait they'll just surround us, or add a guard to the gate." Ronon observed.

"Go now, bat out a hell." Sheppard said breathing heavy.

"Ready?"

"I don't really have a choice now do I." McKay complained and Sheppard took part of his weight so they could hobble as fast as possible.

"On 3." Sheppard ordered and they burst from the cover of the trees and made a mad dash to the DHD. Ronon got there first and put Teyla down gently, drawing his weapon and eyeing the tree line. It took about 4 seconds and there was fire again, stunners aimed right at them. Sheppard continued to shuffle as fast as possible with an injured scientist weighing him down, but they made it. Any time they had managed to gain was lost. McKay began punching symbols as fast as humanly possible while Ronon shot into the trees.

The gate engaged and Rodney sent through his IDC. "Go! Go!" Sheppard yelled and Ronon slung Teyla up into his arms, like a child, and ran for the gate.

"McKay, let's go." Sheppard heaved the man from the DHD and walked them backward to the gate, shooting his P90 haphazardly, and half hoping that they would make it to the gate without any further catastrophes.

With just feet to go to the gate, the high priest burst from the cover of his warriors and moved faster than Sheppard thought humanly possible, shrieking unintelligibly as he rushed them. As the priest cleared the DHD, his shrieks formed words. "Return the Stone! Give me the stone." He reached into a robe made of birds' feathers and pulled out a wicked jagged blade. A weapon like that was not meant to deliver swift death, but existed to rip and tear flesh, causing the most amount of damage as it went in, sawing tissue and organs into fatal wounds. Inflicting incredible amounts of pain before death. The crazed priest drew his arm back and launched himself at the pair.

Sheppard didn't' pause. In one fluid motion he shoved Rodney through the gate and swung his P90 around, pulling the trigger as he went. The priest crumpled as bullets tore into his body at point blank range. A bullet fired from a p90 travels at 850 m/s as it leaves the barrel. At point blank range the bullets ripped straight through the enraged priest, raining blood back down on both of them. Sheppard imagined he could see daylight on the other side of the priest through the holes left by his bullets.

The priest dragged himself forward, hand still extended, even as blood came from his mouth, dripping down his chin. It looked black, a red so dark it couldn't be entirely human. "Stone. Give. Stone." The priest's eyes lost their vibrancy and his knotted hands lost their strength, just as more of the Wraith worshipping warriors clamored around the DHD.

Sheppard pulled himself free of the death grip of the priest and rolled through the gate as a dart impacted the ground by his left hand.

Sheppard rolled into the gate room, "Raise the shield!" He shouted, rolling into a defensive position facing the incoming worm hole. He only relaxed when he saw the glimmer of light indicating the shield was in place. There was a series of sickening thuds, as those who opted to follow him through the gate ran into the shield, like unfortunate bugs hitting a windshield.

"Good God, someone get medical in here!" Woolsey ordered as he descended the stairs. "What happened, Col Sheppard?" He said expectantly.

Ronon igonored the little man and adjusted his grip on Teyla, "Sheppard you hurt?"

"Not mine." Sheppard panted, looking at his blood soaked chest, and slowly sank into the floor, taking great gulps of air. He rolled on his back and looked at the ceiling of the gate room. "McKay?"

"Alive, for the moment." There was silence for a minute, amidst the din of chaos, and then Rodney's voice cut through all the noise. "At least it wasn't a total loss." Sheppard's eye's narrowed in suspicion, the words of the High priest reverberating in his memory.

"What do mean Rodney?" He said as he rolled to his knees and faced the scientist. Rodney was looking enraptured, a foot long glossy black cylinder cradled in his hands. It appeared smooth, and formed entirely of a piece, as though the rock from which it came had simply birthed it in one whole piece instead of it being carved from its face. There was nothing special about it at first glance, but the longer John looked the more he realized that the cylinder seemed to be absorbing light. "What is it and where did you get it?" Sheppard asked.

"Didn't know you liked rocks McKay?" Ronon quipped from the side. Dr. Keller had just arrived and was tending to Teyla, Ronon hovering protectively nearby.

"It's not a rock. At least I'm pretty sure it is not just a rock." McKay said with an air of long suffering.

"Answer my question McKay!" Sheppard ordered rising to his feet and trying to swat away the good intentioned med tech trying to make sure he wasn't full of holes.

"I found it… on the planet."

"right, and by "found" you mena "stole"."

"I prefer an opportunistic adding to the wealth of knowledge in Atlantis." Rodney said a bit indignantly.

"You stole some farmers' holy rock."

"They were wraith worshippers, its better off in my hands than theirs, and." He paused for effect and waggled his fingers at the obsidian cylinder, "It's not a rock." He repeated yet again.

"What is it then?" Woolsey getting his two cents in as he stared fascinated at the cylinder.

"No idea." Sheppard raised his eyebrows and inhaled getting ready to launch into a triad about putting the entire team at risk because of this damned… odd… rock. "Look it's giving off some pretty intense radiation."

"Is it dangerous?" Keller this time, looking up from a now barely awake Teyla.

"No, not that kind of radiation. It's something I'm sure I read about somehwere, but well, once I give this thing enough power, who knows what I'll discover." Rodney exclaimed clearly excited. "Think they'll ship the Noble Prize out here in Pegasus?"

Sheppard took a long calming breath; he was going to need it. "So let me get this straight, you stole a sacred rock from some back water little settlement because it was giving off some kind of weird radiation and you thought it was a good idea to bring it back here."

McKay looked positively radiant. "Yup."

"Didn't think to run it by me first."

"Ah come on, there wasn't any time. It wasn't as if I stole… confiscated… it until after they were going to sacrifice us to the Wraith."

"Glad to know you have some morals." Woolsey added. The poor man looked tired. Sheppard couldn't blame him. Between Ronon being trigger happy and Rodney having quick fingers and a loose tongue, it was a full time job picking up after the Number 1 team on Atlantis. Sheppard felt a fleeting moment of sympathy for the man.

"The lecture will have to wait for later. I want all of you in the infirmary, just to be safe." Keller interrupted. Ronon shrugged and went after the gurney caring Teyla. Rodney seemed to remember that he had hurt himself and switched gears effortlessly from enthused scientist to invalid in the space of one heartbeat.

Sheppard just shook his head, taking up a place at the rear. _It's amazing I don't have grey hair._

* * *

Keller released the team to their own devices after about an hour. Woolsey's debrief wasn't scheduled until Teyla was fit to join them, and Keller wanted to keep her overnight for observation. Apparently whatever the Urosians had painted on their darts was similar to the neurotoxin of the blue ringed octopus. On earth it was a fatal poison with no known antidote. However, Teyla seemed to be recovering fine, with no side effects. Keller was fascinated, convinced that it might be possible to create an antidote for this deadly poison from such a similar toxin. The biochemists would be having the time of their life for another month easy.

Sheppard wandered slowly. He was tired and was half thinking about a snack and some light reading, but his feet had other ideas. Somehow he managed to wander himself to McKay's lab. Of course McKay hadn't even paused for breath, his enthusiasm for his new toy over riding his ankle.

"Figures." Sheppard grumbled a bit and invited himself into McKay's lab.

It was already a flurry of activity. Cables connected to the cylinder, computers diagnosing. Zalenka hovering over a screen and grinning like a child who just found out where mommy and daddy stash the Christmas presents. _Geek's paradise._ Sheppard thought fondly.

McKay had abandoned his crutches and was hobbling around the lab eager anticipation written all over his face.

"So any idea what it is yet?" Sheppard said by way of letting the two scientists know he was there.

"Of course!" Rodney said annoyed as Zalenka shook his head in the negative. Sheppard tried not to smile, but failed miserably.

"Look we're just about to connect power to it, so go… hover… over there." McKay indicated some vague place as far from the device as possible.

Zalenka smiled apologetically and Sheppard shrugged taking up a place near the door, just in case. You could never be too careful when it came to McKay and his harmless little tests. The man had blown up ¾ of a solar system.

"Initiating power…. now."

There was a low humming as the device was infused with power.

"What does it do?" Sheppard asked, genuinely fascinated by the odd device.

"It appears to be emitting more of that radiation. Interesting. Why can't I remember where I heard of it?" Rodney complained mournfully. Sheppard wasn't listening.

Sheppard could hear it, the cylinder, like it was playing music. "Can you heat that?" He asked mesmerized.

"Hear what?" McKay said not really listening.

"You can't hear that? It sounds like music." Sheppard raised his hand and half wondered when he had moved from the door. He wanted to touch it, see if the music changed with his touch, like the device needed him to touch it, that it wanted to play for him and it could do it so much better if he would just touch it.

"Nope don't hear anything." McKay said again still only half paying attention to Sheppard. "Huh, that's strange."

"Yes the radiation levels seem to be increasing." Zalenka chimed in.

"Not harmful." McKay began to snap his fingers repeatedly in excitement. "I just remembered. I think I know what this is," McKay said looking up at Zalenka and snapping his fingers in excitement.

Sheppard had his hand outstretched. The cylinder seemed to be purring, just a bit closer, just a little bit more.

"I think it's like the quantum mirror device back on earth, only maybe a bit different. The same radiation was detected from the mirror. How could I have forgotten. How did the wraith worshippers get it?" McKay then looked back to the devise and Sheppard fingers mere millimeters from brushing its polished ebony surface.

"SHEPPARD DON"T" it was too late, Sheppard's fingers touched it and there was a blinding flash of light. "Touch it." McKay finished. As he blinked trying to remove the spots burned into his retinas, _why doesn't anyone listen to me._ The cylinder was exactly where it had been, more an odd absence of light than an actual object, in the otherwise functional room. The cables were still touching it in various places, but something was conspicuously missing.

"Sheppard?" McKay said, then said it again with emphasis calling down curses for anyone who though it mature to hide like this. He quickly went from annoyed to panicked, bringing up the life signs detector for the city. Counting for people know to be on missions, the city was short one person. He touched his comm. "McKay to Sheppard." There was static.

He hadn't really expected him to answer anyway.

"Where do you think he went?" Zalenka asked quietly.

"Hopefully, somewhere friendly."

Suddenly there was a sound, like great turbines grinding to a halt. The light overhead flickered and died. Atlantis had just lost power. "Oh that is just great!" McKay said exasperated.

"Dr. McKay, what happened?" Woolsey said nearly hysterical over the comm.

"Are you going to tell him?" Zalenka said to the darkness.

"Can't you do it?" McKay whined.

"I do not have death wish."

* * *

TBC... please forgive any spelling/grammar errors. Did my best but sometimes you can't see the forest for the trees.


	3. Chapter 3

Alright here we go. The last 2 chapters were mostly exposition.

I don't own anycharacters except the ones I create. Pity really.

Forgive any spelling or gammar errors, the little beasties sneak up on me sometimes.

* * *

Later he would say the differences had been in the details. Now, in the thick of it, he was plagued a by a sense of "not quite right". It was vague, and not strong enough to cause great alarm. Later, he would say he should have known.

There wasn't enough light. His windows usually let in almost enough moonlight to read by, certainly enough to chase away the ghosts of his past, and the demons in his soul. The bed felt wrong. It was too wide maybe, but all the lumps were in the right places. His feet hung off the end familiarly, but it still felt wrong.

He didn't remember coming to his quarters. He couldn't remember having dinner or even leaving McKay's lab for that matter. He didn't remember falling asleep. He was still dressed, his sidearm pressing uncomfortably into his thigh. Not to mention he was lying on his stomach, a position he didn't usually sleep in, oddly he found it kind of comfortable.

The smell was familiar, a sort of musky earthy man scent that he associated with himself, but there was a counterpoint to it, something fruity and pleasant. Grapefruit maybe, or lemons, mixed with vanilla. He couldn't pinpoint the exact scent, but it was something he associated with women.

The shadows of things looked mostly familiar to his sleep fogged brain, the lumps to the right could be his golf clubs, the large squarish thing against the wall his dresser. _Must have hit my head on the way down that hill. _It made sense, and it wouldn't be the first time.

He began to relax into the familiar, and he was dog tired. He thought about taking his clothes off, but that required effort, effort he just wasn't willing to put out right then. He started at his feet ordering each muscle to relax, working his way up to his head. He was about level with his hips when something intruded on the meditative relaxation.

He heard soft steps. The padding of bare feet on cement floors. He stopped breathing, training taking over. He came fully awake, every instinct in his body screaming that he was in mortal danger. He carefully slipped his leg up from under him, rolling slowly to his side. He flinched as the sheets seemed to make noise under him as he moved. He slowly reached for his sidearm, hoping whoever was in his room didn't notice him in the near complete blackness. He eased the weapon form his thigh, and slowly clicked the safety off.

H couldn't hear the padding of feet, an eerie silence descending over the room. Whoever was moving had stopped, he knew they had heard whatever minimal sounds he had made and were listening.

He had one shot. Surprise was on his side. He let his breath out slowly, willed his heart to slow and counted to 3.

He rolled and sprung from the bed, commanding Atlantis to light the room as he went. He was blinded for a moment as she responded enthusiastically to his will, but so was the unidentified intruder. He was trained for this so he moved before the trespasser had even regained his vision. He quickly had the person wrapped securely by one arm, the gun pressed to the side of his head.

Only it wasn't a he. It was a she, and she was small. The top of her head barely came to his chin.

"What?" She began and he shoved the gun roughly into her temple. Just because she was tiny didn't mean she wasn't dangerous. Teyla had taught him that with countless sound beatings when they sparred.

"Quiet! Who the hell, are you and what are you doing here?" She was silent for so long he thought he was going to have to inspire her to talk. "Answer my question, who are you?" He said roughly. She was shaking, but it could be a rouse.

"Ava." She said breathlessly, "Please don't hurt me." Her hands clung to his forearm. There were hundreds of people on Atlantis, and there was no way he knew everyone by name, but his facial recognition skills were pretty damn good. He released her, keeping the gun tight to her head and turned her around so he could see her face.

She had green eyes, and long dark lashes. Her hair was tied back in a loose ponytail. Her nose was long, and straight, but it suited her face. Under any other circumstances he would have found her attractive. The only problem was he had never seen her before. He was certain of that.

"What are you doing here?" She made no move to answer him, "Answer me!" He growled through clenched teeth, his patience growing thin.

"I'm a doctor." Didn't narrow it down much, there were a lot of those in the city.

"What field?"

"Medical."

He barred his teeth in triumph. "Bad news lady. I've seen every doctor this place has to offer repeatedly and I've never seen you. So let's try this again. Who. Are. You?" Now that he was looking at her he could tell that she was afraid. Her eyes were wide, like McKay's on a mission that went bad. Her lower lip was trembling and she was shaking like a leaf. He moved to brush his comm. and get security in here, but it wasn't there.

_Damn Keller must still have it._ He cursed softly.

Her eyes kept darting to the right, past him. His curiosity was piqued, but he didn't dare take his eyes off her. "What is so interesting over there?"

She shook her head. "Nothing", squeaking past her trembling lips. He smiled dangerously and took a step back, trying to get in a position where he could keep the gun trained on her and find out what was so interesting. Unfortunately his quarters were too small and there was no way to get to a suitable position. So he took a chance, and glanced over his arm at whatever she was looking at. He caught sight of something that really he didn't remember having in his quarters, but had no more time to analyze it further.

She made a move as soon as his attention was diverted, but it was to the left and not what he had been expecting. She snatched something off the left nightstand; he didn't recall having a left nightstand.

"LORNE!" She screamed into the comm. before he was able to tear it from her fingers. What the hell had that been about? He was starting to become very confused. She wasn't supposed to be here, but she had called for Lorne. Things just weren't adding up. He kept the gun trained on the woman, who had descended into tears, and decided to wait for Lorne. Once there was more security things would be sorted out.

It only took a minute and the door opened. Lorne stepped into the room, weapon held tight to his shoulder ready for trouble. "Lorne, great. I found this woman sneaking around my room. Take her to the brig." Lorne had slowly dropped his weapon, the gun held loosely and pointing at the ground, and looked at him, eyes wide mouth hanging open. Teyla came in a second behind him with a security detail. She slowed to a standstill.

It was then things began to spiral out of control.

A baby began to cry. _That defienetly doesn't belong in here!_

Sheppard eyes went wide and he turned looking somewhat behind him. There, on the right, was a bassinet. He ignored the woman walking forward and peering into the cradle. Inside was a tiny baby, with tussled black hair, mouth open in a wail that was quickly turning into full out screaming. _Torren?_

He shook his head in shock. He turned back on the woman and rushed her. She squealed as he grabbed her by the shirt and spinning quicly, slammed her into the wall, near the baby. He didn't even feel bad when her head hit the wall and rebounded. "You were here to take the baby. Unbelievable." The room was tense. "Teyla" he called, "Come and get Torren, this intruder was taking him."

It was a scene from nightmare. Too many guns and one innocent child in the midst of it.

"Torren?" Teyla said, her brow creasing in a moment of confusion, but she recovered quickly. "Of course, my son let me by… John and I'll take him." Sheppard didn't notice the slight hesitation on his name and pulled the woman with him away from the cradle. Teyla slipped by them and picked up the child who was beginning to getting desperate..

"Shhh, Shhh. It's alright. There, I've got him." Teyla said, and the woman, Ava, seemed to wilt. _Hah botched your plan._ Sheppard thought in triumph.

Lorne waited until Teyla and the baby were safely out in the hall. Then he raised his weapon, recovering from his initial shock. "Now how about you drop the gun and let her go." Lorne said gesturing with the p90. There was no mistaking that tone. It was an order.

"What are you doing Major?" Sheppard snapped, emphasiaing the rank of the other man.

"It's Lieut. Col,"

"Since when?" There was a stirring and another familiar face entered the room. "Carson. When did you get back?"

Beckett didn't miss a beat, though his eyes did grow wide with shock, and looked a Lorne. "Easy son, how about we just put down the weapons before someone gets hurt."

"What is going on?" Sheppard said. He was getting tired of asking that question and no one answering him. Beckett just looked at him and Lorne expectantly.

"We're trying to figure this out, Doc." Lorne replied.

"Aye I can see that. But I don't think guns will make it any easier." He gave Sheppard and Lorne both a pointed look. Lorne moved first, lowering his weapon and mumbled, "Fine." And Sheppard lowered his gun and took a step back away from the woman. Ava sobbed and ran, as soon as he was clear of her, out into the hall where Teyla promptly handed over the screaming baby.

Sheppard was even more confused and took a step forward, which was blocked by Lorne. Ava looked at him. She just looked and even he couldn't miss the expression on her face.

Betrayal.

She pressed the baby to her chest and fled down the hall away from everyone.

Lorne glared at him.

"Who are you?" There was no trace of any good humor or tolerance left in Lorne and Sheppard just scowled right back.

"What is wrong with you?" He said folding his arms across his chest.

"Answer the question", Beckett this time, his eyes worried. Maybe it was Beckett that did it, but Sheppard found himself responding, but he didn't remove his finger from the trigger of the gun in his hand.

"LT. col. John Sheppard, of the Atlantis expedition to Pegasus." He watched as Beckett and Lorne exchanged a look. "What?"

"Let's get you to the infirmary, get you checked out."

"I'm fine, but thanks for the concern. What is going on?!" His patience was at its limits.

"Right." Lorne said and raised his weapon and trained it on Sheppard again.

"Col, that isn't going to help." Beckett said pleadingly, hands up in a gesture of peace.

"Sorry Doc, really am, but security is my department, and this has gone on long enough." Beckett sighed and nodded. "Drop the weapon and come with us."

"Lorne I don't know what game you are playing, but as your commanding officer I order you to stand down."

If anything Lorne looked angry, where before he had looked wary and unsure.

"I know 3 things for certain.

1. The sunrise over San Francisco can't be beat for nothing, and I would give my right arm to see it one more time.

2. The ancients were bastards who played with humanity like we were dolls and when it got too much for them they opted out leaving us to deal with their mess.

3. Col" a slight emphasis on the rank. "John Sheppard has been dead for 3 months, so there is no way in hell you could possibly be him."

Sheppard winced. Dead? They all thought he was dead. One look at Teyla and Beckett's expressions confirmed it, they all thought he was dead. Someone had been messign with the memories of everyone he knew. "Well obviously you're wrong about me being dead since I'm standing right HERE!" Sheppard retaliated.

Lorne smiled a glint in his eye. "I don't give a fuck who you think you are, but if you don't drop that weapon I _will _make you drop it."

"Better do as he says, it'll be for the best." Beckett interceded.

Sheppard didn't like the sound of that. He had no choice. So he crouched down, setting the 9mm on the floor and stood up, hands out, a gesture of surrender. These were his people, even if they seemed to be a trifle off, they were still his. He would bide his time. Answers were coming, he could feel it.

* * *

TBC... reviews would be nice, hint hint hint. constructive crit is welcome.


	4. Chapter 4

A brief delay, it's hard to write when looking at a computer screen gives you vertigo.

A HUGE thanks to T-man626 for proof reading

as always don't own

Enjoy

* * *

Dr. Elizabeth Weir looked around the table in the briefing room. There were too many empty chairs. Too many people gone who simply could never be replaced.

Dr. Beckett, Col. Lorne, Drs. Zelenka and Kavanagh, and, of course, Michael and Teyla were all gathered around the table. The _Phoenix_ was on a supply run and wouldn't be back for 2 weeks. _Daedalus_ was in orbit and her commander, a Lt. Miller, was also there. He was young, not terribly experienced, but the simple fact was there was no else for the job. At least he had some flight experience in 302s. There weren't too many who could say that.

There was an air of suppressed urgency in the room, as if everyone there were holding their breath for a miracle. She had quit trusting in miracles.

"Well let's get to the point at hand: our 'guest'. Dr. Beckett, if you would," she said, not mincing words. Carson stood and went to a screen, bringing up an image of a DNA helix spiralung endlessly across the screen, the computer interpretation of the genetic code sequencing below it.

"We took blood and hair samples and compared them to what we had on file."

"And?"

"I don't know how else to say it, but they are a perfect match. There appears to be no damage to the genetic code, nothing to indicate cloning or tampering of any kind. He even has the ATA gene. According to every medical test I can perform, he is in fact John Sheppard."

There was silence around the room. "How is this even possible?" she asked to a general nodding of heads.

Beckett simply shrugged. "There is no easy answer to that I am afraid."

"How's Ava?" Weir continued, her voice soft and full of concern.

He smiled a bit sadly. "I had to administer a mild sedative. She demanded to be present when I ran the tests, and predictably didn't take it well. She's resting now, one of the staff close by. This has been extremely difficult for her." Weir didn't doubt it, it wasn't everyday your dead husband came back to life and pulled a gun on you with your infant son in the room.

Weir nodded. "It has been for us all. I can only imagine what she is going through." There was another pause and Weir continued, "So the question remains, what we do with… the current occupant of the brig?"

"You all know what I think," Lorne stated emphatically.

"Yes, but we can't just leave him on some planet, wish him the best of luck and move on," Weir reprimanded gently.

"Not to mention he has the ATA gene, and we could really use an extra set of hands," Kavanagh reminded everyone.

"That may be so, but can he be trusted? We have no idea where he came from, or how he came to be, no idea where his loyalties lie." It was Michael this time, Lorne nodding in approval beside him.

There was silence for a while, no one else willing to venture out an opinion. "Well clearly it is time I met out guest. Col. Lorne, if you'd do the honors."

* * *

Sheppard paced restlessly across the cell. It was a perfect square, 10 paces by 10 paces. Something was very wrong with the people on the base. _Why is it always up to me_? he asked silently, shaking his head as his feet continued their back and forth motion. First thing was to get out of the brig. Unfortunately he knew all too well that getting out was impossible. Unless you had McKay with you, which sadly he didn't.

He felt a sudden pang of worry. He hadn't seen McKay yet. Little red flags went up. Why hadn't he seen McKay, or Ronon for that matter? McKay was always in the thick of everything that went on in Atlantis, albeit because it was usually his fault, but Ronon was also fiercely protective of the city. He should have responded when Lorne did. There was an answer there. He could feel it, hovering just out of reach.

His thoughts were interrupted as the doors opened and his feet immediately stopped.

"Oh this day just gets better and better," he said, hands coming to rest on his hips. The position was meant to make him look more intimidating, broadening his chest and making him seem bigger than he was. It usually worked, on McKay anyway. The woman who stood looking at him, hands clasped together, a familiar smile barely there on her lips didn't look particularly intimidated, only curious. Lorne hovered a pace behind her.

"And why would you say that?" Dr. Weir said.

"Well for starters, you're dead."

"No more than you it would seem," she replied, raising her eyebrows in a gesture that was so familiar it was downright spooky.

He came up short, no witty remark popping into his head. She had him there. What had Lorne said, something about knowing three things for certain and one of them was that he was dead? He shrugged, walked over to the bunk, and sat down with his back to the low bed. If she couldn't be intimidated, he might as well pretend to be comfortable.

Weir began to circle his cage. He remembered doing the same thing on several occasions. It was unnerving when you were on the receiving end of it.

"You know this usually goes better if you actually ask me some questions," he said, not really believing for a moment that this person was in fact Elizabeth Weir. No matter how much she sounded like her or looked like her. It just couldn't be her.

"I only have one question: who are you?"

"What, Beckett's tested didn't come back?" he asked sarcastically. Maybe this was another replicator trick.

"Oh they're back."

"And?" Maybe the Wraith had found another Ancient dream device.

"According to everything Dr. Beckett has been able to test you are John Sheppard."

"All right there we go, now that that's been cleared up how about letting me out of the cage?" He knew full well that there was no way in hell she'd actually do it.

She smiled a half-hearted smile and said nothing, just circled the cell and looked him.

"It's unbelievable," she said after a long silence. "You look like him, sound like him, even walk like him. You _are_ him right, down to the DNA."

"I sense a 'but' coming."

But she didn't continue. Her finger went to her ear and she appeared to be listening to something. Lorne did as well. He hated not being in the loop, especially when he was the object of debate. He knew that just by watching their faces.

"Very well" Weir said, and not to him. "If you will excuse us… John…."

"Hey if you're going could you grab a pizza? Coffee? Beer?"

Weir smiled again, that oh-so-familiar grin. "We'll see what we can do." And then he was alone. The cell was still 10 paces by 10 paces.

* * *

Dr. Weir walked swiftly towards the science labs. Dr. Zelenka said he had solved the mystery. Lorne stalked silently beside her.

"You don't like him." A statement not a question.

"No ma'am."

"He is John." All evidence pointed that way no matter how little sense it actually made.

"That man is not John Sheppard. I don't care what the Doc's tests say." She didn't push the Colonel, but let it go. This was one thing everyone was going to have deal with on their own, in their own way.

They passed in hurried silence until they stood before Dr. Zelenka and Michael. Michael gestured for Radek to begin; he just stood there, a self-satisfied smile spreading from ear to ear. They waited.

And they waited.

"Anytime Dr. Zelenka." Weir encouraged, unable to hide the exasperated smile that sprang from nowhere. There were so few reason to truly smile these days, she took what she could get.

"I believe I have figured out who he is." Dr. Beckett sidled over, curious. "According to all available data he is indeed John Sheppard, but there are a few very minor differences."

"That's not so, every test says his DNA is identical."

"I am not disputing your findings, Carson. I have found a few tiny things that differentiate our Sheppard from this one."

"Continue," Weir said, and Radek brought up a wave length.

"What you are looking at is benign radiation. It is harmless. We were all exposed to it when our gate exploded 2 years ago. The intensity has been gradually decreasing, and so has the concentration in our cells."

"I can confirm that," Dr. Beckett volunteered, bringing relief to those present.

The display changed, showing two sets of cells, one on top and one beneath. "The one on top is a sample from Col. Sheppard taken a few weeks before… before his death. His levels are roughly the same as ours. The second is from the samples Dr. Beckett took today. The levels are much higher, suggesting his exposure to the exploding gate was much more recent."

Weir desperately just wanted Radek to get to the end and make his announcement of what he found. Unfortunately, she hadn't seen the Czech so animated in too long. She couldn't take this from him. "So you are saying he's from our past?"

"No."

"Aye, I can confirm that. If he were truly from our past his cells would be younger, but they aren't. They appear to be the same in chronological age as Col. Sheppard."

"Ok. If not from our past, then what?" Weir continued.

Radek smiled like a cat. "Are you aware of the scientist Hugh Everett?"

She thought for a second. "No, sorry."

"Of course, I didn't actually expect you to be, he postulated that we do not exist in a single universe but a..." he paused, looking for the word, "...multi-verse."

"A multi-verse." Weir wasn't following.

"Yes. He theorized that for every choice made, the opposite choice was made somewhere else. Like a die. It can land on any of it's 6 sides, and in 6 different universes a different face is seen. Example, in our universe you chose to head up the Atlantis team, in another..."

"I didn't. So in another Universe someone else runs the Atlantis program." The idea was mind boggling. The possibilities were truly endless.

"Of course this has always been just a theory as there has never been a way, which we know of, to test the hypothesis." Radek stopped and gestured for Michael to take over.

"My people have never thought on such terms, so I will admit this idea was entirely novel to me. However, in trying to solve the puzzle of Mr. Sheppard, I have been going over sensor reading for yesterday around the time of his arrival. There is a definite anomaly. A massive amount of energy is built up and then released. The energy does not come from us in any way. I checked: the power levels have not changed since yesterday, nothing to account for this massive amount of power. Atlantis registers another life sign, but because Sheppard is known it does not raise any alarms."

"It came from Dr. McKay's lab."

"So you think this energy means that Dr. McKay was working on some device, managed to _get _it working, and it caused this John Sheppard to come through from a different universe into ours?" Weir could not keep the incredulity out of her voice.

"Exactly. It is the only thing that makes any sense, however improbable this sounds."

There was general silence for a moment. Then Beckett spoke. "So his cells have higher concentrations of the radiation because his gate exploded more recently for him than us."

Radek smiled triumphantly.

"This is simply incredible," Beckett continued.

"Well, Dr. Zelenka, I am just going to have to take your word for it," Weir responded, patting the little man's arm in appreciation.

"Dr. Weir, this doesn't solve anything. Great we have an idea, he's from another universe. One we don't know anything about. We still have to answer the question, What do we do with him?" Lorne pointed out.

It was a good question.

* * *

Sheppard was starting to think of all the ways he was going to get even with Rodney. He didn't know what he would be getting even for, but he was certain that it was McKay's fault. Something had made all of his people screwy. Then, to top it off, there was Elizabeth: walking, talking, looking-exactly-like-Elizabeth. It had to be Rodney. Maybe it was that cylinder. It wouldn't be the first time that man's curiosity caused some major problems.

The doors opened. "Speak of the devil," he said ambivalently, and stopped pacing.

"Hello John," she said simply. Beckett, Zelenka and Lorne followed a step behind; they clearly respected her. "Lorne, would you please let him out."

"Now we're getting somewhere."

"We have concluded that you are in fact who you say you are," she informed him as the field was let down and the door opened. "And not."

"'And not?' What the hell does that mean?"

"Are you familiar with alternate realities?"

"Of course, we all met Rod." They all looked at him blankly, "Nice guy, McKay from another reality. We were all there, same time we met his sister, Jeannie." Still blank looks. "What the hell is wrong with all of you?"

Dr. Zelenka spoke quickly, "We believe you are from a parallel universe."

"Yeah right. You'll understand if I don't believe you."

"Think about it, it makes sense. To us you are dead, you said yourself that I am dead," Weir replied with a sudden pain in her chest. It was strange to think of a place that could exist where she was dead.

Sheppard hadn't stepped out of the cell, even though his freedom beckoned. "Where's McKay?"

The group looked between each other finally settling on Lorne who shrugged and answered. "No harm in that information: he's dead."

"Dead?"

Strangely it was the thought of the obnoxious scientist being dead that sold him on the parallel universe theory. It was easier to keep thinking "not Rodney, not the Rodney I know" than "dead". It explained Elizabeth alive, walking talking and being characteristically Elizabeth, a Lorne so different than the man he knew (the word harsh came to mind).

"Parallel universe. Ok, let's say I'm willing to believe you for the moment, now what?" He stepped out of the cell and crossed his arms across his chest.

Zelenka smiled and pushed his glasses up his nose, bringing out a tablet. "Have you ever seen this before?"

It was a picture of a black cylinder, a cylinder that seemed to be less than really there, as if light simply bent around it instead of actually interacting with it. "Yeah. McKay stole it from a planet we visited a couple of days ago."

Zelenka was nearly bouncing. "We found this here in one of the labs. Apparently the Ancients were experimenting with creating a bridge between universes. Dr. McKay was working on it shortly before he… died." Zelenka's enthusiasm seemed to shrink, and then he rallied after a moment. "We believe that the ancients succeeded, but abandoned the project because of complications."

"Yeah, Rodney succeeded in creating a bridge between universes, which resulted in Rod coming for a visit."

"He did it without the device?" Zelenka sounded incredulous.

"This is all fascinating, Dr. Zelenka," Weir interrupted.

"Yes, yes. What did you do with it?"

"Nothing. I just touched it," Sheppard replied trying to remember what had happened. "Yeah, McKay had it wired up to a power source and it started making music of some kind and I just touched it. It was kind of weird."

Dr. Zelenka was silent for a moment. "Music. McKay did not put that in any of his reports," Zelenka said as he began flipping through text again. "Well that is neither here nor there. It is clearly activated by the Ancient gene."

"Great. So all I have to do is touch it, you hook up some juice and Bob's your uncle, Mary's your aunt, I'm home."

There was a creepy sense to the silence that followed. Sheppard's enthusiasm went down a few notches, but he just wanted to get home.

"I am afraid it is not that simple," Weir said. "From what Dr. Zelenka has shown me the power required to activate the device is incredible."

"So, hook it up to the ZPM, you do have one right?"

"We..." she began.

"That is not crucial information for him to know," Lorne interrupted.

"Fine. We cannot afford the power to send you back."

Sheppard's heart sank into his toes. "What do you mean you can't afford the power?" His voice rose at the end.

"Look, I don't know how things are going where you are from, but here they are pretty serious."

"The Elizabeth I knew wouldn't hesitate to help me out." It was a low blow, and he knew it, but she didn't even hesitate. She drew breath and he was reminded again why so many people willingly followed this woman.

"I cannot and will not put the people of _this_ city in danger just to send you home. The concerns of this base are my primary responsibility. I am sorry. I really am."

Thing was, that was the Elizabeth he knew. She would willingly sacrifice those under her command for the greater good, and no matter that he was John Sheppard, he wasn't _their_ John Sheppard.

"So what you gonna do, just keep me here?"

"Well we wanted to offer you the chance to help us. We have limited numbers of people with the Ancient gene and we could really use you around here."

"And if I refuse, you just gonna ship me back to Earth to live out my days in the comfort of the SGC brig? That how it's going to go?"

There was a long silence, and everyone looked uncomfortable. Lorne nodded, giving approval. "I am afraid that won't be possible."

"And why's that?"

"Earth is gone."

* * *

"Dr. McKay where is Col Sheppard?" Mr. Woolsey said forcibly.

McKay was trying his best not to look sheepish. "Look if the flyboy hadn't touched it..."

"Where!" Woolsey interrupted.

"Um, parallel universe, I think."

"You think?" Teyla sounded disapproving.

"I'm ninety-nine percent certain. Look as far as I can tell the device is goes to one place and one place only."

"How can you be certain?" Woolsey asked.

"Look the math is really complicated and you're just going to have to trust me. All we have to do is wire up some more power and send someone, such as myself, through so I can reactivate the device on the other side and bring him back."

Woolsey stood up to his full height and sat down behind his desk stiff as a board. "Unfortunately, Dr. McKay that is not going to be possible."

"What?" Ronon barked, menacing the sitting man.

"We have no idea where he went. We don't even know if he is alive."

"Sheppard is alive," Ronon said with certainty.

"There is simply no way to know that," Woolsey continued, trying his best to look not intimidated. "And there is the small fact that using the device the first time," McKay opened his mouth to start his defense, Woolsey overrode him, "however unintentional, nearly depleted the ZPM. We only have power now because of the generators."

"Are you saying Sheppard isn't worth it?" Ronon growled.

"No, Sheppard is an irreplaceable member of Atlantis, and his loss is tragic. However I cannot risk any other member of this base on the slim chance, and it _is_ a slim chance, that he is even alive."

"Fine I'll volunteer. I'm not a member of your precious base and so you can't be held responsible for my actions." Ronon said, standing tall and looking as imposing as possible.

Woolsey sighed and clasped his hands in front of him on the immaculate desk. "Be that as it may, the power consumption on the device is tremendous. We just don't have the power."

"We'll find another ZPM." McKay stated emphatically.

"Really, where? I know you want to bring Col Sheppard back, but I am afraid that this time, he is on his own."

* * *

TBC.... reviews make the world go round... hint... hint


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